Interdisciplinary Team Creates Way to Capture RNA From Living Cells

January 7, 2014

A multidisciplinary team from Penn has published in Nature Methods a first-of-its-kind way to isolate RNA from live cells in their natural tissue microenvironment without damaging nearby cells. This allows the researchers to analyze how cell-to-cell chemical connections influence individual cell function and overall protein production.

The identity and function of individual cells within each tissue type—heart, skin, and brain, for example—are closely linked by which genes are transcribed into RNA and, ultimately, proteins.Most knowledge about variability in gene expression has been from studies using heterogeneous groups of cells grown in culture. Researchers doubt the ability to extrapolate “real biology” from these unnatural conditions. Tools for counting and characterizing RNA provide a unique opportunity to assess how mammalian cells work, and can also provide insight into how that function may go awry in various diseases and eventually help in testing new drugs.

James Eberwine, Elmer Holmes Bobst Professor of Pharmacology in the Perelman School of Medicine and co-director of the Penn Genome Frontiers Institute (PGFI), and Ivan Dmochowski, Associate Professor of Chemistry, led this study. Other Penn co-authors include Jai-Yoon Sul, Research Assistant Professor of Pharmacology; M. Sean Grady, Charles Harrison Frazier Professor of Neurosurgery, and PGFI co-director Junhyong Kim, Edmund J. and Louise W. Kahn Endowed Term Professor in the Natural Sciences in the Department of Biology.

Their technique is called TIVA. The team used this method to physically isolate the RNA of a single cell within living tissue in mouse and human cells by “tagging” or capturing the RNA with a custom-built molecule. The TIVA tag is a Swiss Army Knife type of molecule, designed to contain the multiple chemical tools it needs to accomplish its task of capturing messenger RNA, or mRNA, from a cell without getting any from its neighbors.

The TIVA approach promises to highlight important aspects of human neurobiology and disease without first isolating human neurons. The team is currently developing additional TIVA tags with distinct functional groups so that multiple tags can be put into the same cell or multiple cells and the dynamics of how different molecules function in single cells can be quantified and compared in their natural tissue.

The research was supported by the PhRMA foundation, the National Institutes of Health and a McKnight Foundation Technology Innovations Award. This project is also funded, in part, by the Penn Genome Frontiers Institute under a grant with the Pennsylvania Department of Health.

In collaboration with Robert Carpick and David Goldsby, Tian, who graduated from Penn in 2017 with a doctorate in physics, recently published a paper in Physical Review Letters which attempts to tackle these devastating natural phenomena by investigating the laws of friction at the smallest possible scale, the nanoscale.

A leader in the fields of plant biology, chromatin modification, and epigenetics, Wagner’s research focuses on understanding at the molecular level the complex changes that occur when an organism switches developmental programs.